Table 2 Parameters
Parameter | explanation | Values |
|---|---|---|
\(L^2\) | lattice size | \(500 \times 500\) lattice sites |
T | Boltzmann temperature | 16 AUE |
\(\lambda\) | cell stiffness | 4.0 AUE/[lattice site]\(^2\) |
\(A_T\) | cell target area | 50 lattice sites |
Cell adhesion | ||
    \(J_\alpha\) | minimum J value between cells | 4 AUE/[lattice site length] |
    \(J_\alpha '\) | minimum J value between cell and medium | 8 AUE/[lattice site length] |
    \(\nu\) | length of receptor and ligand bitstring | 24 bits |
    \(\nu '\) | length ligand bitstring for medium adhesion | 6 bits |
Cell migration and chemotaxis | ||
    \(\mu _p\) | strength of persistent migration | 3.0 AUE |
    \(\tau _p\) | duration of persistence vector | 50 MCS |
    \(\mu _{\chi }\) | strength of chemotaxis | 1.0 AUE |
    \(k_{\chi }\) | scaling factor chemoattractant gradient | 5.0 molecules/[lattice site length] |
Cell division | ||
    \(\eta _{\text {init}}\) | time before cell in GRN state 1 can start growing | 10000 MCS |
    \(\eta _{\text {grow}}\) | time for cell in state 1 to grow to 2x \(A_T\) and divide | 20000 MCS |
Evolution | ||
    \(\tau _s\) | duration of season | \(18 \times 10^4\) - \(50 \times 10^4\) MCS |
    \(p_{\text {min}}\) | minimum probability of dying | 0.05 |
    \(p_{\text {max}}\) | maximum probability of dying | 1.0 |
    \(d_{\text {scale}}\) | distance from gradient peak where death probability is \(\frac{1}{2}\) maximum | 40 or 80 [lattice site length] |
    \(\mu _{R,I}\) | receptor and ligand mutation probability | 0.01 per bit, per replication |
    \(\mu _{\omega }\) | mutation probability of network parameters (w, f, \(r_a\)) | 0.02 per parameter, per replication |
    \(\sigma\) | standard deviation of mutation size | 0.05 |